5WKT | pdb_00005wkt

3.2-Angstrom In situ Mylar structure of bovine opsin at 100 K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.295 (Depositor), 0.298 (DCC) 
  • R-Value Work: 
    0.274 (Depositor), 0.278 (DCC) 
  • R-Value Observed: 
    0.275 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions.

Broecker, J.Morizumi, T.Ou, W.L.Klingel, V.Kuo, A.Kissick, D.J.Ishchenko, A.Lee, M.Y.Xu, S.Makarov, O.Cherezov, V.Ogata, C.M.Ernst, O.P.

(2018) Nat Protoc 13: 260-292

  • DOI: https://doi.org/10.1038/nprot.2017.135
  • Primary Citation Related Structures: 
    5VRA, 5WJK, 5WKT

  • PubMed Abstract: 

    Protein crystallography has significantly advanced in recent years, with in situ data collection, in which crystals are placed in the X-ray beam within their growth medium, being a major point of focus. In situ methods eliminate the need to harvest crystals, a previously unavoidable drawback, particularly for often small membrane-protein crystals. Here, we present a protocol for the high-throughput in situ X-ray screening of and data collection from soluble and membrane-protein crystals at room temperature (20-25°C) and under cryogenic conditions. The Mylar in situ method uses Mylar-based film sandwich plates that are inexpensive, easy to make, and compatible with automated imaging, and that show very low background scattering. They support crystallization in microbatch and vapor-diffusion modes, as well as in lipidic cubic phases (LCPs). A set of 3D-printed holders for differently sized patches of Mylar sandwich films makes the method robust and versatile, allows for storage and shipping of crystals, and enables automated mounting at synchrotrons, as well as goniometer-based screening and data collection. The protocol covers preparation of in situ plates and setup of crystallization trials; 3D printing and assembly of holders; opening of plates, isolation of film patches containing crystals, and loading them onto holders; basic screening and data-collection guidelines; and unloading of holders, as well as reuse and recycling of them. In situ plates are prepared and assembled in 1 h; holders are 3D-printed and assembled in ≤90 min; and an in situ plate is opened, and a film patch containing crystals is isolated and loaded onto a holder in 5 min.


  • Organizational Affiliation
    • Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.

Macromolecule Content 

  • Total Structure Weight: 42.36 kDa 
  • Atom Count: 2,842 
  • Modeled Residue Count: 337 
  • Deposited Residue Count: 359 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rhodopsin348Bos taurusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P02699 (Bos taurus)
Explore P02699 
Go to UniProtKB:  P02699
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02699
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Transducin Galpha peptide11Bos taurusMutation(s): 0 

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
4N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD
GlyCosmos: G81315DD
GlyGen: G81315DD
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose
D
2N/A
Glycosylation Resources
GlyTouCan: G92130SN
GlyCosmos: G92130SN

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.295 (Depositor), 0.298 (DCC) 
  • R-Value Work:  0.274 (Depositor), 0.278 (DCC) 
  • R-Value Observed: 0.275 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 242.043α = 90
b = 242.043β = 90
c = 110.637γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyBR 5124/1-1
Canada Excellence Research Chair ProgramCanada--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM108635

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-01-17
    Changes: Database references
  • Version 1.2: 2020-01-01
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary